Identification of genetic variants in patients with ischemic stroke : a multi-omic analysis

Author(s)

Amanda Donatti

• Document type: Doctoral Thesis
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Faculdade de Ciências Médicas
• Defense date: 2021-03-22

Examining board members

Íscia Teresinha Lopes Cendes; Mônica Barbosa de Melo; Wilson Nadruz Junior; Viviane Hiroki Flumignan Zetola; Adriana Bastos Conforto

• Advisor: Íscia Teresinha Lopes Cendes; Rodrigo Secolin

Abstract

Stroke is one of the most frequent diseases worldwide and one of the leading causes of death and disability. Ischemic stroke is the most common subtype, affecting around 80% of the patients. Although environmental risk factors have been established to increase the risk of stroke, they contribute only with approximately 60% of the probability of developing the disease. Thus, genetic factors also play a role in the predisposition to stroke. Some studies identified common genetic variants putatively associated with stroke. However, it is also possible that rare variants may contribute to the heritability of the disorder. Furthermore, stroke is a multifactorial disorder, where it is expected an interaction of different genetic and environmental factors to determine the biological alterations leading to disease. These interactions can create molecular biomarkers that, in turn, may be used in clinical practice to assist in the diagnose or to establish disease prognosis. In this way, distinct risk factors might converge to determine common molecular mechanisms, which may affect gene expression regulation in patients with stroke. Therefore, the aims of this study are: i) to evaluate the contribution of rare genetic variants to the risk of developing ischemic stroke; ii) to determine the circulating microRNAs expression pattern in patients with ischemic stroke, in both the acute and chronic stage of the disease; and iii) to determine the metabolomic pattern on plasma samples from patients with ischemic stroke, in both the acute and chronic stage of the disease. Using next-generation sequencing, we evaluated the exome of 130 patients with ischemic stroke, the plasma microRNA expression pattern of 154 individuals, including 53 controls, and the metabolomic pattern from the plasma of 52 individuals, including 14 controls. The exome analysis allowed us to identify 523 rare variants in 53 genes of interest to ischemic stroke, from which we highlight COL4A3, COL6A3, FGFR2, FVIII, HLA-B. These genes are primarily part of the following biological pathways: collagen biosynthesis, blood coagulation, inflammation, angiogenesis, and vascular integrity. Furthermore, we identified circulating microRNAs with a differential expression in different phases of ischemic stroke. The microRNAs let-7, mir-182, and mir-324 were differentially expressed in the acute phase of stroke. In contrast, mir-34c was differentially expressed in the chronic phase of ischemic stroke. Comparing the microRNAs expression pattern on acute and chronic phases, we observed changes in expression levels of microRNAs mir-142, mir-16, mir-206, and mir-30a. We also observed similarities between microRNAs identified in plasma and those associated exclusively with extracellular vesicles. We identified metabolites associated with acute stroke in plasma of patients by NMR techniques, such as formate, pyruvate, and GlycA. During the chronic phase, the level of glutamate was altered in patients when compared to controls. Interestingly, the metabolites identified as differentially abundant in patients are related to similar biological pathways as the microRNAs found to be differentially expressed in patients. In conclusion, we identified rare variants in candidate genes, as USP7, which were not previously identified to ischemic stroke, that may predict the risk of occurrence and the severity of ischemic stroke. Also, we identified circulating microRNAs and metabolites specific for the different stages of ischemic stroke, and that have not been observed in ischemic stroke patients, that should be validated in broader clinical studies. These molecules are potential disease biomarkers and might help, in the future, the development of new strategies to prevent, diagnose and treat patients with ischemic stroke. (AU)

• FAPESP's process: 15/25607-0 - Identification of Rare Genomic Variants and microRNAs expression patterns in stroke patients
• Grantee: Amanda Donatti
• Support Opportunities: Scholarships in Brazil - Doctorate